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Bio-Design Automation in Synthetic Biology


The creation of complex systems whether electronic, mechanical, chemical, or biological can prove incredibly challenging. Engineering principles such as abstraction, standardization, and formalism have the ability to make this creation process easier, cheaper, faster, and more efficient. Synthetic Biology, the forward engineering of novel biological systems, is an excellent candidate for these types of approaches. In this talk, I will outline my vision for “Bio-Design Automation” for synthetic biology. Specifically I will highlight my research’s efforts in the specification, design, assembly, verification, and data management involved in automating synthetic biology. These challenges are addressed by a suite of software tools which draw inspiration from Electronic Design Automation. I will highlight a domain specific language for synthetic biology called Eugene, an automated DNA assembly planner called Raven, and a liquid handling scheduling system called Puppeteer. In addition I will discuss logic synthesis techniques for synthetic biology (Cello), hybrid microfluidic bio-computation (Fluigi), and my work with undergraduate outreach through the International Genetically Engineered Machine (iGEM) competition. I will close by discussing community and commercial involvement mechanisms via the Bio-Design Automation Consortium, the Nona Research Foundation, and Lattice Automation, Inc.



Douglas Densmore is a Kern Faculty Fellow, a Hariri Institute for Computing and Computational Science and Engineering Junior Faculty Fellow, and Associate Professor in the Department of Electrical and Computer Engineering at Boston University.

He is the director of the Cross-disciplinary Integration of Design Automation Research (CIDAR) group at Boston University, where his team of staff and postdoctoral researchers, undergraduate interns, and graduate students develop computational and experimental tools for synthetic biology. His research facilities include both a computational workspace in the Department of Electrical and Computer Engineering as well as experimental laboratory space in the Boston University Center of Synthetic Biology (CoSBI).

His research interests include Computer Architecture, Embedded Systems, Logic Synthesis, Digital Logic Design, System Level Design, and Synthetic Biology. His research focuses on the development of tools for the specification, design, and assembly of synthetic biological systems, drawing upon his experience with embedded system level design and electronic design automation (EDA). Extracting concepts and methodologies from these fields, he aims to raise the level of abstraction in synthetic biology by employing standardized biological part-based designs which leverage domain specific languages, constraint based device composition, visual editing environments, and automated assembly.